I guess my problem is that, for example, Artillery weapons such as long-range missiles and sniper rifles (especially sniper rifles) can end up doing damage to the target without scratching the cover. So I can shoot a guy behind a wall with my sniper rifle, without damaging the wall.

Thanks for the input, Rafial - you are very possibly correct. I'm interested to see what Vincent says as well.

It's easy for me to imagine a sniper mech getting a bead on a mech behind a wall (by its electronic or heat signature, maybe) and shooting it through the wall. The wall's value as cover is the protection the wall provides. It's also easy for me to imagine the shot punching a little hole in the wall without affecting the wall's value as cover (which is what damaging it would mean).

Yeah, that's it exactly, when you are talking giant mechs on the battlefield, you can assume so many ways to acquire targets that don't require visual, and all ranged weapons capable of indirect fire. As a counterpoint, I'll mention the unfairly ignored game Battlesuit, which was a man-to-man powered armor infantry game set in the Ogre universe. In that game, you can always shoot at anybody on the map, lack of LOS simply adds a bit of a penalty.